📄 1mvm.pdb
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REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REMARK 200 REPLACEMENT REMARK 200 SOFTWARE USED: PURDUE REMARK 200 STARTING MODEL: CANINE PARVOVIRUS (MONOCLINIC FORM) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 1/2+X,1/2+Y,Z REMARK 290 4555 1/2-X,1/2+Y,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 194.84112 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 208.33333 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 111.15280 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 194.84112 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 208.33333 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 111.15280 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE REMARK 300 THE VIRUS PARTICLE HAS A PROTEIN SHELL WITH ICOSAHEDRAL REMARK 300 SYMMETRY. EACH ICOSAHEDRAL UNIT CONTAINS ONE PROTEIN REMARK 300 SUBUNIT, VP-2. TO GENERATE A VIRAL SHELL FROM THE REMARK 300 COORDINATES GIVEN BELOW REQUIRES GENERATING THE OTHER REMARK 300 ICOSAHEDRAL UNITS. THIS IS ACCOMPLISHED BY APPLYING THE REMARK 300 532 POINT GROUP SYMMETRY ELEMENTS IN THE SPECIFIC ORDER REMARK 300 5X2X3X2 ABOUT SPECIFIC AXES WHOSE TRANSFORMATIONS ARE GIVEN REMARK 300 BELOW. THE FOLLOWING FOUR STEPS ARE TO BE APPLIED TO REMARK 300 EACH POLYPEPTIDE CHAIN. EACH OF THE TOTAL 60 SYMMETRY REMARK 300 OPERATIONS ARE DERIVED BY CONSECUTIVE APPLICATION OF THE REMARK 300 ROTATIONAL SYMMETRY OPERATORS. REMARK 300 REMARK 300 THE LAST TWO-FOLD AXIS IS COINCIDENT WITH THE REMARK 300 CRYSTALLOGRAPHIC TWO-FOLD AXIS ALONG THE B MONOCLINIC AXIS. REMARK 300 THEREFORE, ONLY 30 VP-2 SUBUNITS ARE CRYSTALLOGRAPHICALLY REMARK 300 INDEPENDENT AND THE REMAINING 30 CAN BE GENERATED BY THE C2 REMARK 300 SPACE GROUP SYMMETRY. HOWEVER, THERE ARE TWO PARTICLE REMARK 300 CENTERS CRYSTALLOGRAPHICALLY INDEPENDENT IN THE ASYMMETRIC REMARK 300 UNIT OF THE UNIT CELL AND EACH OF THEM HAS 30 ASSOCIATED REMARK 300 VP-2 SUBUNITS, MAKING A TOTAL NUMBER OF 60 INDEPENDENT VP-2 REMARK 300 SUBUNITS IN THE MONOCLINIC UNIT CELL. REMARK 300 REMARK 300 IN CONCLUSION, TO GENERATE THE WHOLE PROTEIN SHELL OF THE REMARK 300 VIRUS IN A STANDARD ORIENTATION (60 COPIES) THE FOUR POINT REMARK 300 GROUP SYMMETRY ELEMENTS DESCRIBED BELOW (5X2X3X2) SHOULD BE REMARK 300 APPLIED IN THE SPECIFIC ORDER. TO GENERATE THE WHOLE REMARK 300 PACKING OF THE VIRUS IN THE MONOCLINIC C2 UNIT CELL ONLY REMARK 300 THE FIRST THREE SYMMETRY ELEMENTS SHOULD BE APPLIED TO REMARK 300 OBTAIN 30 INDEPENDENT COPIES OF VP-2 IN ORTHOGONAL REMARK 300 COORDINATES (SEE BELOW FOR THE DESCRIPTION TO GENERATE THE REMARK 300 FRACTIONAL CRYSTALLOGRAPHIC COORDINATES). REMARK 300 REMARK 300 LET P1 = COORDINATES OF ANY ATOM AS LISTED IN ENTRY REMARK 300 REMARK 300 1. REMARK 300 TRNSF1 1 0.500000 0.809017 0.309017 REMARK 300 TRNSF2 1 -0.809017 0.309017 0.500000 REMARK 300 TRNSF3 1 0.309017 -0.500000 0.809017 REMARK 300 REMARK 300 APPLY THE FIVE-FOLD GIVEN BY TRNSF 1 REMARK 300 REMARK 300 P1 = P1 REMARK 300 P2 = TRNSF 1 * P1 REMARK 300 P3 = TRNSF 1 * P2 REMARK 300 P4 = TRNSF 1 * P3 REMARK 300 P5 = TRNSF 1 * P4 REMARK 300 REMARK 300 P1 THROUGH P5 CONSTITUTE AN ENTIRE PENTAMER, REMARK 300 CONSISTING OF FIVE PROTOMERIC UNITS. ONE COMPLETE REMARK 300 PENTAMER SET OF COORDINATES WILL CONTAIN FIVE CHAINS REMARK 300 OF VP-2. REMARK 300 REMARK 300 2. REMARK 300 TRNSF1 2 0.000000 1.000000 0.000000 REMARK 300 TRNSF2 2 0.000000 0.000000 1.000000 REMARK 300 TRNSF3 2 1.000000 0.000000 0.000000 REMARK 300 REMARK 300 FIRST, APPLY THE THREE-FOLD GIVEN BY TRNSF 2 TO EACH REMARK 300 OF THE FIVE PROTOMERS P1 THROUGH P5 TO GENERATE REMARK 300 P6 THROUGH P10. FOR EXAMPLE, REMARK 300 REMARK 300 P6 = TRNSF 2 * P1 REMARK 300 P7 = TRNSF 2 * P2 REMARK 300 P8 = TRNSF 2 * P3 REMARK 300 P10 = TRNSF 2 * P5 REMARK 300 REMARK 300 PROTOMERS P11 THROUGH P15 MAY BE GENERATED REMARK 300 BY APPLYING TRNSF 2 TO PROTOMERS P6 TO P10. REMARK 300 FOR EXAMPLE, REMARK 300 REMARK 300 P11 = TRNSF 2 * P6 REMARK 300 P12 = TRNSF 2 * P7 REMARK 300 P13 = TRNSF 2 * P8 REMARK 300 P15 = TRNSF 2 * P10 REMARK 300 REMARK 300 3. REMARK 300 TRNSF1 3 -1.000000 0.000000 0.000000 REMARK 300 TRNSF2 3 0.000000 -1.000000 0.000000 REMARK 300 TRNSF3 3 0.000000 0.000000 1.000000 REMARK 300 REMARK 300 APPLY THE TWO-FOLD GIVEN BY TRNSF 3 TO P1 THROUGH P15 REMARK 300 TO GENERATE P16 THROUGH P30 FOR A COMPLETE HEMISPHERE REMARK 300 REMARK 300 P16 = TRNSF 3 * P1 REMARK 300 P17 = TRNSF 3 * P2 REMARK 300 P18 = TRNSF 3 * P3 REMARK 300 P19 = TRNSF 3 * P4 REMARK 300 P30 = TRNSF 3 * P15 REMARK 300 REMARK 300 4. REMARK 300 REMARK 300 TRNSF1 4 -1.000000 0.000000 0.000000 REMARK 300 TRNSF2 4 0.000000 1.000000 0.000000 REMARK 300 TRNSF3 4 0.000000 0.000000 -1.000000 REMARK 300 REMARK 300 FINALLY, APPLY THE TWO-FOLD GIVEN BY TRNSF 4 (AND REMARK 300 COINCIDENT WITH THE CRYSTALLOGRAPHIC TWO-FOLD AXIS) REMARK 300 TO EACH OF THE THIRTY PROTOMERS (WILL YIELD A TOTAL REMARK 300 OF SIXTY UNITS, THE WHOLE VIRAL CAPSID). FOR REMARK 300 EXAMPLE, REMARK 300 REMARK 300 P31 = TRNSF 4 * P1 REMARK 300 P32 = TRNSF 4 * P2 REMARK 300 P41 = TRNSF 4 * P11 REMARK 300 P51 = TRNSF 4 * P21 REMARK 300 P60 = TRNSF 4 * P30 REMARK 300 REMARK 300 THIS YIELDS A TOTAL OF 60 PROTOMERS IN AN ICOSAHEDRAL REMARK 300 VIRION. REMARK 300 REMARK 300 TO OBTAIN THE FRACTIONAL CRYSTALLOGRAPHIC COORDINATES, REMARK 300 XCRYST, FROM THE CARTESIAN MOLECULAR COORDINATES, XCART, ⌨️ 快捷键说明
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